Research workbench
Crystal structure of a de novo designed trimeric coiled-coil peptide
Analyse Crystal structure of a de novo designed trimeric coiled-coil peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HQJ
- Type
- protein
- Length
- 180 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sin-asp-glu-leu-glu-ala-arg-ile-arg-glu-leu-glu-ala-arg- ile-lys-NH2
- Ligands
- PB, SO4
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 87% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Sin-asp-glu-leu-glu-ala-arg-ile-arg-glu-leu-glu-ala-arg- ile-lys-NH2 | protein | 15 | 87% helix, 0% strand | — |
Ligands and binding sites
- PB · Lead (II) ion · metal · 9 copies · chains A, D, F, C, E, H, K, L
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D, E, F, H, I, K, L
- SIN · Succinic acid · additive · 12 copies · chains A, K, L, B, C, D, E, F, G, H, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 177 | 0.63 | 0.84 | 25 | SIN, PB |
| 2 | 151 | 0.52 | 0.80 | 26 | SIN |
Interfaces
29 interfaces between chains.
- E–F · 414 Ų buried · 4 hydrogen bonds · protein-protein
- J–L · 408 Ų buried · 4 hydrogen bonds · protein-protein
- G–H · 395 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 389 Ų buried · 5 hydrogen bonds · protein-protein
- D–E · 374 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 covalent (additive adduct).
Compared structures
- 1HQJ · Crystal structure of a de novo designed trimeric coiled-coil peptide · the same entry in another collection · chain J against J, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 1HQJ · PDBe 1HQJ
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